Name: Three Cheese Manicotti Bake Recipe
Prep time: 30 min
Cook time: 40 min
Total time: 1 h 10 min
Cuisine: Italian-American
Ingredients: 1 (8 ounce) box manicotti shells (14 pasta shells); 1 tablespoon olive oil; 32 ounces ricotta cheese; 4 garlic cloves, minced or grated; 2½ cups shredded mozzarella cheese (9 ounces); 1 cup grated Parmesan cheese, divided (4 ounces); ½ cup chopped fresh basil; ½ teaspoon salt; ¼ teaspoon ground black pepper; ¼ teaspoon ground nutmeg; 2 large eggs; 3 cups marinara sauce (24 ounces), homemade or store bought

If you’re looking for a comforting, crowd-pleasing Italian dish that brings cheesy, saucy goodness to your table, look no further than this Three Cheese Manicotti Bake Recipe. I absolutely love how this turns out—rich ricotta, gooey mozzarella, and sharp Parmesan all mingle perfectly inside tender pasta shells, baked in a flavorful marinara sauce. Once you try it, you’ll see why my family goes crazy for this recipe, and I bet it’ll become a staple in your rotation too!

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Why You’ll Love This Recipe

Triple Cheese Delight: The mix of ricotta, mozzarella, and Parmesan makes each bite decadently rich and flavorful.
Perfect Texture: Parboiling the manicotti shells ensures they finish perfectly tender without turning mushy.
Family Friendly: It’s a surefire hit with kids and adults alike, making family dinners stress-free and delicious.
Make Ahead Friendly: You can prepare it in advance and freeze it—ideal for busy weeks or special occasions.

A white baking dish filled with seven folded pasta shells arranged in two rows. Each shell is stuffed with a white creamy filling and topped with bright red tomato sauce that is chunky and spread in small piles along the top. Fresh green basil leaves and small bits of grated white cheese are scattered on top, adding color contrast. The thick red sauce lines the bottom and sides of the dish, and the pasta shells have a ridged texture and a soft yellow color. The dish sits on a white marbled surface. Photo taken with an iphone --ar 2:3 --v 7 - Three Cheese Manicotti Bake, cheesy manicotti casserole, Italian baked pasta, cheesy manicotti recipe, family-friendly Italian dinner

Ingredients You’ll Need

These ingredients blend beautifully to create a perfectly balanced filling and sauce combo. A bit of fresh basil really lifts the flavors, so I recommend using it whenever possible.

Flat lay of uncooked manicotti pasta shells arranged neatly, a small white bowl of olive oil, a mound of fresh ricotta cheese, four whole garlic bulbs cloves separated but unpeeled, shredded mozzarella cheese in a small white ceramic bowl, grated parmesan cheese in a small white bowl, a small bunch of fresh basil leaves, two large whole brown eggs with clean shells, and a small white bowl filled with bright red marinara sauce, all placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997 - Three Cheese Manicotti Bake, cheesy manicotti casserole, Italian baked pasta, cheesy manicotti recipe, family-friendly Italian dinner

Manicotti shells: Look for the classic pre-formed pasta tubes—you want about 14 to fill your casserole dish nicely.
Olive oil: Just a drizzle to keep the cooked pasta from sticking and to add a touch of richness.
Ricotta cheese: The creamy base of the filling; full fat works best for richness.
Garlic cloves: Freshly minced or grated for the best bold, aromatic flavor.
Mozzarella cheese: Shredded; it melts nicely and makes the dish wonderfully gooey.
Parmesan cheese: Divided use—half mixed in the filling and half for sprinkling on top.
Fresh basil: Adds a fresh, herby brightness that complements the cheese and tomato sauce beautifully.
Salt: Essential to bring out the flavors in the cheese and sauce.
Black pepper: Freshly ground for a subtle warming kick.
Nutmeg: A tiny bit adds warmth and depth to the cheese filling—don’t skip it!
Large eggs: Helps bind the filling so it holds together perfectly when baked.
Marinara sauce: Homemade or store-bought, choose a sauce with rich tomato flavor and good seasoning.

Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Variations

I like to mix things up depending on who I’m cooking for or what I have on hand. Feel free to personalize this Three Cheese Manicotti Bake Recipe to suit your taste, whether that’s adding veggies or tweaking the cheese blend.

Spinach Addition: I often fold chopped fresh spinach into the filling for a boost of color and nutrition—my family barely notices and loves the extra flavor.
Meat Lover’s Version: Ground Italian sausage or cooked ground beef can be stirred into the sauce or filling for a heartier meal.
Herb Variations: Swap out basil for fresh oregano or parsley based on what you have; it’s a simple change that adds variety.
Gluten-Free Option: Use gluten-free manicotti shells or roll your own pasta sheets for a GF-friendly version that’s just as delicious.

How to Make Three Cheese Manicotti Bake Recipe

Step 1: Prep and Parboil the Manicotti Shells

Start by bringing a large pot of salted water to a boil. Cooking the manicotti shells for just 6 to 7 minutes is key—they should be slightly tender but still firm (al dente). I learned the hard way that overcooked shells get mushy and tear when you fill them! Once cooked, drain and toss them gently with a drizzle of olive oil to keep them from sticking together. Set them aside and let cool while you prepare the cheese filling.

Step 2: Make the Three Cheese Filling

In a large bowl, combine ricotta, two cups of shredded mozzarella, half of the grated Parmesan, minced garlic, chopped fresh basil, salt, pepper, and just a pinch of nutmeg. In a small dish, whisk the eggs, then gently fold them into the cheese mixture to bind everything together. The filling should be luscious but not runny—this balance makes stuffing easier and the final bake holds its shape beautifully.

Step 3: Fill and Arrange the Manicotti

Spread about one and a half cups of marinara sauce evenly on the bottom of your greased 13×9-inch baking dish. Here’s a trick I discovered: scoop half of your cheese filling into a zip-top bag, snip off a small corner, and pipe the filling directly into each manicotti shell—this makes the process faster and neater than spooning. Arrange the filled shells snugly in the sauce. Repeat until all shells are stuffed and placed in the dish.

Step 4: Bake and Cheese It Up

Pour the remaining marinara sauce over the filled manicotti. Cover the dish with foil (pro tip: spray the foil lightly with non-stick spray to prevent cheese from sticking) and bake at 350°F for 20 minutes. Then, remove the foil and bake an additional 10 to 15 minutes until it’s bubbly and cooked through. Finally, sprinkle the remaining mozzarella and Parmesan cheese over the top and bake for 5 more minutes until melted and golden. Garnish with a bit of fresh basil for that perfect finishing touch.

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Pro Tips for Making Three Cheese Manicotti Bake Recipe

Don’t Overcook the Pasta: Parboiling shells just until tender keeps them from becoming mushy after baking.
Filling Made Easy: Using a piping bag or plastic bag corner cut makes stuffing neat and quick.
Sauce Coverage Matters: Make sure your sauce fully coats all shells to keep them moist and flavorful.
Avoid Crowding: Give your manicotti room in the pan to prevent them from sticking or bursting.

How to Serve Three Cheese Manicotti Bake Recipe

Three Cheese Manicotti Bake Recipe - Serving

Garnishes

I love to garnish this dish with a sprinkle of freshly chopped basil or a handful of torn fresh basil leaves to brighten the rich cheese flavors. Sometimes, I add a dusting of extra Parmesan for those who want a cheesier finish. A pinch of red pepper flakes on the side adds a nice kick for spice lovers.

Side Dishes

We often pair this manicotti bake with lightly dressed mixed greens or a Caesar salad to cut through the richness. Garlic bread or warm focaccia is another favorite—perfect for soaking up any leftover marinara sauce on the plate. Roasted or steamed veggies like asparagus or broccoli make a simple, nourishing addition too.

Creative Ways to Present

For special occasions, I’ve served individual manicotti pieces on pretty dinner plates garnished with basil and a drizzle of extra virgin olive oil. Another fun idea is to bake the manicotti in mini ramekins for personal portions—everyone feels fancy, and cleanup’s easy!

Make Ahead and Storage

Storing Leftovers

Leftover manicotti reheats beautifully. I store mine in an airtight container in the fridge, and it keeps well for about 3 to 4 days. The flavors actually deepen after a day, so it’s a tasty next-day lunch or dinner option.

Freezing

This Three Cheese Manicotti Bake Recipe freezes like a dream. Simply assemble everything in a freezer-safe dish, cover tightly with plastic wrap and foil, and freeze for up to 3 months. When you’re ready to enjoy, bake it from frozen at 350°F for about an hour—or until hot and bubbly. This trick saves so much time on busy nights!

Reheating

To reheat, cover your leftovers with foil and warm in a 350°F oven until heated through, about 20 minutes. If you’re in a hurry, the microwave works too, but the oven keeps that signature baked texture and cheese melt best. Adding a splash of marinara before reheating helps maintain moisture.

FAQs

Can I use no-boil manicotti shells in this recipe?

You can, but I prefer to parboil regular manicotti shells for the best texture. No-boil shells can sometimes become gummy or unevenly cooked, so if you use them, make sure your sauce is extra saucy and give the dish a bit more baking time.
Is this recipe freezer-friendly?

Yes! This Three Cheese Manicotti Bake Recipe freezes wonderfully. Assemble, cover tightly, and freeze for up to 3 months. Bake from frozen at 350°F until bubbly and heated through—super convenient for meal prepping.
What can I substitute for ricotta cheese if I’m allergic?

You can substitute ricotta with cottage cheese blended smooth or even a soft tofu mixture for a dairy-free option. Just make sure to adjust seasoning to keep the flavor balanced.
Can I prepare the filling ahead of time?

Absolutely! You can mix the cheese filling up to a day ahead and keep it refrigerated until you’re ready to stuff the shells. It saves time and can help the flavors meld.

Final Thoughts

This Three Cheese Manicotti Bake Recipe is one of those dishes that never fails to bring comfort to the table. I’ve made it countless times for family dinners, potlucks, and even weeknight meals when I want something a little indulgent but easy. If you’re looking for a recipe that combines cheesy, saucy, and tender pasta in one dish, this is your winner. Give it a try—you’ll be making it again and again, I promise.